Extracting genomic feature sequences from GTF/GFF files with AGAT

Tutorial:Extracting genomic feature sequences from GTF/GFF files with AGAT

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3.6 years ago

Juke34 8.9k

First install AGAT:

conda create -c bioconda -n agat agat 
conda activate agat

Then enjoy possibilities of agat_sp_extract_sequences.pl, below exemplified

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GFF corresponding to the record used as reference: enter image description here

extract GTF GFF sequence • 6.5k views

ADD COMMENT • link updated 2.2 years ago by eggrandio ▴ 40 • written 3.6 years ago by Juke34 8.9k

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A great toolkit in Perl, kudos for that!

ADD REPLY • link 3.6 years ago by Michael 55k

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I assume this retrieves the sequence, but I was wondering if it's possible to retrieve an annotated version of the sequence, for example, in Genbank format, where the introns and exons are mapped. I would find that extremely useful.

By the way. thank you for creating AGAT, it has saved me many headaches when using GFF files!

ADD REPLY • link 2.2 years ago by eggrandio ▴ 40

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